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Items: 1 to 20 of 22


Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes.

Meldal BHM, Bye-A-Jee H, Gajdoš L, Hammerová Z, Horácková A, Melicher F, Perfetto L, Pokorný D, Lopez MR, Türková A, Wong ED, Xie Z, Casanova EB, Del-Toro N, Koch M, Porras P, Hermjakob H, Orchard S.

Nucleic Acids Res. 2018 Oct 24. doi: 10.1093/nar/gky1001. [Epub ahead of print]


Interleukins and their signaling pathways in the Reactome biological pathway database.

Jupe S, Ray K, Roca CD, Varusai T, Shamovsky V, Stein L, D'Eustachio P, Hermjakob H.

J Allergy Clin Immunol. 2018 Apr;141(4):1411-1416. doi: 10.1016/j.jaci.2017.12.992. Epub 2018 Feb 21.


Reactome graph database: Efficient access to complex pathway data.

Fabregat A, Korninger F, Viteri G, Sidiropoulos K, Marin-Garcia P, Ping P, Wu G, Stein L, D'Eustachio P, Hermjakob H.

PLoS Comput Biol. 2018 Jan 29;14(1):e1005968. doi: 10.1371/journal.pcbi.1005968. eCollection 2018 Jan.


Reactome diagram viewer: data structures and strategies to boost performance.

Fabregat A, Sidiropoulos K, Viteri G, Marin-Garcia P, Ping P, Stein L, D'Eustachio P, Hermjakob H.

Bioinformatics. 2018 Apr 1;34(7):1208-1214. doi: 10.1093/bioinformatics/btx752.


The Reactome Pathway Knowledgebase.

Fabregat A, Jupe S, Matthews L, Sidiropoulos K, Gillespie M, Garapati P, Haw R, Jassal B, Korninger F, May B, Milacic M, Roca CD, Rothfels K, Sevilla C, Shamovsky V, Shorser S, Varusai T, Viteri G, Weiser J, Wu G, Stein L, Hermjakob H, D'Eustachio P.

Nucleic Acids Res. 2018 Jan 4;46(D1):D649-D655. doi: 10.1093/nar/gkx1132.


Reactome enhanced pathway visualization.

Sidiropoulos K, Viteri G, Sevilla C, Jupe S, Webber M, Orlic-Milacic M, Jassal B, May B, Shamovsky V, Duenas C, Rothfels K, Matthews L, Song H, Stein L, Haw R, D'Eustachio P, Ping P, Hermjakob H, Fabregat A.

Bioinformatics. 2017 Nov 1;33(21):3461-3467. doi: 10.1093/bioinformatics/btx441.


Reactome pathway analysis: a high-performance in-memory approach.

Fabregat A, Sidiropoulos K, Viteri G, Forner O, Marin-Garcia P, Arnau V, D'Eustachio P, Stein L, Hermjakob H.

BMC Bioinformatics. 2017 Mar 2;18(1):142. doi: 10.1186/s12859-017-1559-2.


The Reactome pathway Knowledgebase.

Fabregat A, Sidiropoulos K, Garapati P, Gillespie M, Hausmann K, Haw R, Jassal B, Jupe S, Korninger F, McKay S, Matthews L, May B, Milacic M, Rothfels K, Shamovsky V, Webber M, Weiser J, Williams M, Wu G, Stein L, Hermjakob H, D'Eustachio P.

Nucleic Acids Res. 2016 Jan 4;44(D1):D481-7. doi: 10.1093/nar/gkv1351. Epub 2015 Dec 9.


Expression data analysis with Reactome.

Jupe S, Fabregat A, Hermjakob H.

Curr Protoc Bioinformatics. 2015 Mar 9;49:8.20.1-9. doi: 10.1002/0471250953.bi0820s49.


A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology.

Porras P, Duesbury M, Fabregat A, Ueffing M, Orchard S, Gloeckner CJ, Hermjakob H.

Proteomics. 2015 Apr;15(8):1390-404. doi: 10.1002/pmic.201400390. Epub 2015 Mar 21. Review.


The complex portal--an encyclopaedia of macromolecular complexes.

Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S.

Nucleic Acids Res. 2015 Jan;43(Database issue):D479-84. doi: 10.1093/nar/gku975. Epub 2014 Oct 13.


The Reactome pathway knowledgebase.

Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, Caudy M, Garapati P, Gillespie M, Kamdar MR, Jassal B, Jupe S, Matthews L, May B, Palatnik S, Rothfels K, Shamovsky V, Song H, Williams M, Birney E, Hermjakob H, Stein L, D'Eustachio P.

Nucleic Acids Res. 2014 Jan;42(Database issue):D472-7. doi: 10.1093/nar/gkt1102. Epub 2013 Nov 15.


Annotating cancer variants and anti-cancer therapeutics in reactome.

Milacic M, Haw R, Rothfels K, Wu G, Croft D, Hermjakob H, D'Eustachio P, Stein L.

Cancers (Basel). 2012 Nov 8;4(4):1180-211. doi: 10.3390/cancers4041180.


Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations.

Ndegwa N, Côté RG, Ovelleiro D, D'Eustachio P, Hermjakob H, Vizcaíno JA, Croft D.

Database (Oxford). 2011 Oct 23;2011:bar047. doi: 10.1093/database/bar047. Print 2011.


The Reactome BioMart.

Haw RA, Croft D, Yung CK, Ndegwa N, D'Eustachio P, Hermjakob H, Stein LD.

Database (Oxford). 2011 Oct 19;2011:bar031. doi: 10.1093/database/bar031. Print 2011.


Reactome pathway analysis to enrich biological discovery in proteomics data sets.

Haw R, Hermjakob H, D'Eustachio P, Stein L.

Proteomics. 2011 Sep;11(18):3598-613. doi: 10.1002/pmic.201100066.


Reactome: a database of reactions, pathways and biological processes.

Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, Matthews L, Caudy M, Garapati P, Gopinath G, Jassal B, Jupe S, Kalatskaya I, Mahajan S, May B, Ndegwa N, Schmidt E, Shamovsky V, Yung C, Birney E, Hermjakob H, D'Eustachio P, Stein L.

Nucleic Acids Res. 2011 Jan;39(Database issue):D691-7. doi: 10.1093/nar/gkq1018. Epub 2010 Nov 9.


The systematic annotation of the three main GPCR families in Reactome.

Jassal B, Jupe S, Caudy M, Birney E, Stein L, Hermjakob H, D'Eustachio P.

Database (Oxford). 2010 Jul 29;2010:baq018. doi: 10.1093/database/baq018.


R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases.

Antonov AV, Schmidt EE, Dietmann S, Krestyaninova M, Hermjakob H.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W78-83. doi: 10.1093/nar/gkq482. Epub 2010 Jun 2.


The Proteomics Identifications database: 2010 update.

Vizcaíno JA, Côté R, Reisinger F, Barsnes H, Foster JM, Rameseder J, Hermjakob H, Martens L.

Nucleic Acids Res. 2010 Jan;38(Database issue):D736-42. doi: 10.1093/nar/gkp964. Epub 2009 Nov 11.

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